microarray 2004


Bibliography on
Microarray Data Analysis

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© Copyright, 1999-2007 Wentian Li
of North Shore LIJ Research Institute

http://www.nslij-genetics.org/microarray/
2004

  1. Boris Adryan, Reinhard Schuh (2004), "Gene-Ontology-based clustering of gene expression data", Bioinformatics, 20(16):2851-2852.
    [abstract]

  2. AA Ahmed, M Vias, NG Iyer, C Caldas, JD Brenton (2004), "Microarray segmentation methods significantly influence data precision", Nucleic Acids Research, 32(5):e50.

  3. Roxana Alexandridis, Shili Lin, and Mark Irwin (2004), "Class discovery and classification of tumor samples using mixture modeling of gene expression data-a unified approach", Bioinformatics, 20(16):2545-2552.
    [abstract]

  4. F Al-Shahrour, R Diaz-Uriarte, J Dopazo (2004), "FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes", Bioinformatics, 20(4):578-580.

  5. R. S. Anderssen, Y. Wu, R. Dolferus, and I. Saunders (2004), "An a posteriori strategy for enhancing gene discovery in anonymous cDNA microarray experiments", Bioinformatics, 20:1721-1727.
    [abstract]

  6. Alexey V. Antonov, Igor V. Tetko, Michael T. Mader, Jan Budczies, Hans W. Mewes (2004), "Optimization models for cancer classification: extracting gene interaction information from microarray expression data", Bioinformatics, 20(5):644-652.
    [abstract]

  7. Sanju Attoor, Edward R. Dougherty, Yidong Chen, Michael L. Bittner, Jeffrey M. Trent (2004), "Which is better for cDNA-microarray-based classification: ratios or direct intensities", Bioinformatics, 20(16):2513-2520.
    [abstract]

  8. Kyounghwa Bae and Bani K. Mallick (2004), "Gene selection using a two-level hierarchical Bayesian model", Bioinformatics, 20:3423-3430.

  9. David Baird, Peter Johnstone, and Theresa Wilson (2004), "Normalization of microarray data using a spatial mixed model analysis which includes splines", Bioinformatics, 20:3196-3205.
    [abstract]

  10. CA Ball, A Brazma, H Causton, S Chervitz, R Edgar, P Hingamp, JC Matese, H Parkinson, J Quackenbush, M Ringwald, SA Sansone, G Sherlock, P Spellman, C Stoeckert, Y Tateno, R Taylor, J White, N Winegarden (2004), "Submission of microarray data to public repositories", PLoS Biology, 2(9):E317.

  11. C Ball, A Brazma, H Causton, S Chervitz, R Edgar, P Hingamp, JC Matese, C Icahn, H Parkinson, J Quackenbush, M Ringwald, SA Sansone, G Sherlock, P Spellman, C Stoeckert, Y Tateno, R Taylor, J White, N Winegarden, Microarray Gene Expression Data (MGED) Society (2004), "An open letter on microarray data from the MGED Society", Microbiology, 150(11):3522-3524.

  12. Karla V. Ballman, Diane E. Grill, Ann L. Oberg, and Terry M. Therneau (2004), "Faster cyclic loess: normalizing RNA arrays via linear models", Bioinformatics, 20(16):2778-2786.
    [abstract]

  13. affymetrix
    Yoseph Barash, Elinor Dehan, Meir Krupsky, Wilbur Franklin, Marc Geraci, Nir Friedman, and Naftali Kaminski (2004), "Comparative analysis of algorithms for signal quantitation from oligonucleotide microarrays", Bioinformatics, 20:839-84.
    [abstract]

  14. Ziv Bar-Joseph (2004), "Analyzing time series gene expression data", Bioinformatics, 20(16): 2493-2503.

  15. Nabil Belacel, Miroslava Cuperlovic-Culf, Mark Laflamme, and Rodney Ouellette (2004), "Fuzzy J-Means and VNS methods for clustering genes from microarray data", Bioinformatics, 20:1690-1701.
    [abstract]

  16. Monica Benito, Joel Parker, Quan Du, Junyuan Wu, Dong Xiang, Charles M. Perou, JS Marron (2004), "Adjustment of systematic microarray data biases", Bioinformatics, 20:105-114.
    [abstract]

  17. TL Bergemann , RJ Laws , F Quiaoit , LP Zhao (2004), "A statistically driven approach for image segmentation and signal extraction in cDNA microarrays", Journal of Computational Biology, 11(4):695-713.

  18. Sven Bergmann, Jan Ihmels, Naama Barkai (2004), "Similarities and differences in genome-wide expression data of six organisms", PLoS Biology, 2(1):85-93.

  19. P Berman, P Bertone, B DasGupta, M Gerstein, MY Kao, M Snyder (2004), "Fast optimal genome tiling with applications to microarray design and homology search", Journal of Computational Biology, 11:766-85.

  20. Madhuchhanda Bhattacharjee, Colin C. Pritchard, Peter S. Nelson, Elja Arjas (2004), "Bayesian integrated functional analysis of microarray data", Bioinformatics, 20:2943-2953.
    [abstract]

  21. David R Bickel (2004), "Error-rate and decision-theoretic methods of multiple testing: which genes have high objective probabilities of differential expression?", Statistical Applications in Genetics and Molecular Biology, 3(1):8.
    [abstract]

  22. David R. Bickel (2004), "Degrees of differential gene expression: detecting biologically significant expression differences and estimating their magnitudes", Bioinformatics, 20(5):682-688.
    [abstract]

  23. R Blanco, P Larrañaga, I Inza, B Sierra (2004), "Gene selection for cancer classification using wrapper approaches", International Journal of Pattern Recognition and Artificial Intelligence, 18(8):1373-1390.
    [abstract]

  24. Benjamin Milo Bolstad (2004), Low-level Analysis of High-density Oligonucleotide Array Data: Background, Normalization and Summarization Ph.D Thesis (University of California, Berkeley).
    [PDF]

  25. Anne-Laure Boulesteix (2004), "PLS dimension reduction for classification with microarray data", Statistical Applications in Genetics and Molecular Biology, 3(1):33.
    [ abstract]

  26. John Boyle (2004), "SeqExpress: desktop analysis and visualization tool for gene expression experiments", Bioinformatics, 20:1649-1650.
    [abstract]

  27. Ulisses M Braga-Neto, Edward R Dougherty (2004), "Is cross-validation valid for small-sample microarray classification?", Bioinformatics, 20(3):374-380.
    [ abstract]

  28. Ulisses Braga-Neto, Ronaldo Hashimoto, Edward R Dougherty, Danh V Nguyen, Raymond J Carroll (2004), "Is cross-validation better than resubstitution for ranking genes?", Bioinformatics, 20(2): 253-258.
    [ abstract]

  29. Leonid Brodsky, Andrei Leontovich1, Michael Shtutman, Elena Feinstein (2004), "Identification and handling of artifactual gene expression profiles emerging in microarray hybridization experiments", Nucleic Acids Research, 32(4):e46.
    [html]

  30. Philippe Broët, Alex Lewin, Sylvia Richardson, Cyril Dalmasso, Henri Magdelenat (2004), "A mixture model-based strategy for selecting sets of genes in multiclass response microarray experiments", Bioinformatics, 20(16):2562-2571.
    [abstract]

  31. Jean-Philippe Brunet, Pablo Tamayo, Todd R Golub, Jill P Mesirov (2004), "Metagenes and molecular pattern discovery using matrix factorization", Proceedings of the National Academy of Sciences, 101(12):4164-4169.
    [abstract]

  32. R Bueno, KR Loughlin, MH Powell, GJ Gordon (2004), "A diagnostic test for prostate cancer from gene expression profiling data", Journal of Urology, 171:903-906.

  33. affymetrix
    Conrad J Burden, Yvonne E Pittelkow, Susan R Wilson (2004), "Statistical analysis of adsorption models for oligonucleotide microarrays", Statistical Applications in Genetics and Molecular Biology, 3(1):35.
    [ abstract]

  34. Anne-Sophie Carpentier, Alesandra Riva, Pierre Tisseur, Gilles Didier, Alain Henaut (2004), "The operons, a criterion to compare the reliability of transcriptome analysis tools: ICA is more reliable than ANOVA, PLS and PCA", Computational Biology and Chemistry, 28:3-10.
    [ abstract]

  35. affymetrix
    Dung-Tsa Chen, Sue-Hwa Lin, and Seng-jaw Soong (2004), "Gene selection for oligonucleotide array: an approach using PM probe level data", Bioinformatics, 20:854-86.
    [abstract]

  36. James J Chen, Robert R Delongchamp, Chen-An Tsai, Huey-miin Hsueh, Frank Sistare, Karol L Thompson, Varsha G Desai, James C Fuscoe (2004), "Analysis of variance components in gene expression data", Bioinformatics, 20:1436-1446.

  37. Cheng Cheng, Stanley B. Pounds, James M. Boyett, Deqing Pei, Mei-Ling Kuo, and Martine F. Roussel (2004), "Statistical significance threshold criteria for analysis of microarray gene expression data", Statistical Applications in Genetics and Molecular Biology, 3(1):36.

  38. Jill Cheng, Shaw Sun, Adam Tracy, Earl Hubbell, Joseph Morris, Venu Valmeekam, Andrew Kimbrough, Melissa S. Cline, Guoying Liu, Ron Shigeta, David Kulp, Michael A. Siani-Rose (2004), "NetAffx Gene Ontology Mining Tool: a visual approach for microarray data analysis", Bioinformatics, 20:1462-1463.

  39. HyungJun Cho, Jae K. Lee (2004), "Bayesian hierarchical error model for analysis of gene expression data", Bioinformatics, 20:2016-2025.
    [abstract]

  40. JH Cho, D Lee, JH Park, IB Lee (2004), "Gene selection and classification from microarray data using kernel machine", FEBS Letters, 571(1-3):93-98.

  41. affymetrix
    Hui-Hsien Chou, An-Ping Hsia, Denise L. Mooney, Patrick S. Schnable (2004), "Picky: oligo microarray design for large genomes", Bioinformatics, 20:2893-2902.

  42. affymetrix
    Tzu-Ming Chu, B.S. Weir, and Russell D. Wolfinger (2004), "Comparison of Li-Wong and loglinear mixed models for the statistical analysis of oligonucleotide arrays", Bioinformatics, 20(4):500-506.
    [abstract]

  43. GA Churchill (2004), "Using ANOVA to analyze microarray data", Biotechniques, 37(2):173-175, 177.

  44. affymetrix
    Leslie M Cope, Rafael A Irizarry, Harris A Jaffee, Zhijin Wu, Terence P Speed (2004), "A benchmark for Affymetrix GeneChip expression measures", Bioinformatics, 20(2): 323-331.
    [ abstract]

  45. L da F Costa, MS Barbosa, ETM Manoel, J Streicher, GB Müller (2004), "Mathematical characterization of three-dimensional gene expression patterns", Bioinformatics, 20:1653-1662.
    [abstract]

  46. M Cronin, K Ghosh, F Sistare, J Quackenbush, V Vilker, C O'Connell (2004), "Universal RNA reference materials for gene expression", Clinical Chemistry, 50(8):1464-1471.

  47. R. Keira Curtis, Martin D. Brand (2004), "Analysing microarray data using modular regulation analysis", Bioinformatics, 20:1272-1284.
    [abstract]

  48. Susmita Datta, Glen A Satten, Dale J Benos, Jiazeng Xia, Martin J Heslin, Somnath Datta (2004), "An empirical bayes adjustment to increase the sensitivity of detecting differentially expressed genes in microarray experiments", Bioinformatics, 20(2):235-242.
    [ abstract]

  49. Jorge García de la Nava, Sacha van Hijum, Oswaldo Trelles (2004), "Saturation and quantization reduction in microarray experiments using two scans at different sensitivities", Statistical Applications in Genetics and Molecular Biology, 3(1):11.
    [abstract]

  50. Marcel Dettling (2004), "BagBoosting for tumor classification with gene expression data", Bioinformatics, 20:3583-3593.

  51. Marcel Dettling and Peter Bühlmann (2004) "Finding predictive gene groups from microarray data", Journal of Multivariate Analysis, 90(1):106-131.
    [abstract]

  52. Lori E. Dodd, Edward L. Korn, Lisa M. McShane, G.V.R. Chandramouli, Eric Y. Chuang (2004), "Correcting log ratios for signal saturation in cDNA microarrays", Bioinformatics, 20:2685-2693.
    [abstract]

  53. Ciprian Doru Giurcaneanu, Ioan Tabus (2004), "Cluster structure inference based on clustering stability with applications to microarray data analysis", EURASIP Journal on Applied Signal Processing, 2004(1):64-80.
    [abstract]

  54. Ciprian Doru Giurcaneanu, Ioan Tabus, Jaakko Astola , Juha Ollila , Mauno Vihinen (2004), "Fast iterative gene clustering based on information theoretic criteria for selecting the cluster structure", Journal of Computational Biology, 11(4):660-682.

  55. I Dozmorov, N Knowlton, Y Tang, M Cantola (2004), "Statistical monitoring of weak spots for improvement of normalization and ratio estimates in microarrays", BMC Bioinformatics, 5:53.
    [abstract]

  56. S Draghici, D Chen, J Reifman (2004), "Applications and challenges of DNA microarray technology in military medical research", Mil Med., 169(8):654-659.

  57. M. Dugas, S. Merk, S. Breit, P. Dirschedl (2004), "mdclust - exploratory microarray analysis by multidimensional clustering", Bioinformatics, 20:931-936.
    [abstract]

  58. Blythe P Durbin, David M Rocke (2004), "Variance-stabilizing transformations for two-color microarrays", Bioinformatics, 20(5):660-667.
    [abstract]

  59. Steffen Durinck, Joke Allemeersch, Vincent J. Carey, Yves Moreau, and Bart De Moor (2004), "Importing MAGE-ML format microarray data into BioConductor", Bioinformatics, 20:3641-3642.

  60. Benjamin L Ebert, Todd R Golub (2004), "Genomic approaches to hematologic malignancies", Blood, 104(4):923-932.
    [abstract]

  61. Paul HC Eilers, Jelle J Goeman (2004), "Enhancing scatterplots with smoothed densities", Bioinformatics, 20(5):623-628.
    [abstract]

  62. Claus Thorn Ekstrøm, Søren Bak, Charlotte Kristensen, and Mats Rudemo (2004), "Spot shape modelling and data transformations for microarrays", Bioinformatics, 20:2270-2278.

  63. HM Fathallah-Shaykh, B He, LJ Zhao, A Badruddin (2004), "Mathematical algorithm for discovering states of expression from direct genetic comparison by microarrays", Nucleic Acids Research, 32(13):3807-3814.

  64. A Fazel Famili, Ganming Liu, Ziying Liu (2004), "Evaluation and optimization of clustering in gene expression data analysis", Bioinformatics, 20:1535-1545.

  65. Jian-Bing Fan, Joanne M. Yeakley, Marina Bibikova, Eugene Chudin, Eliza Wickham, Jing Chen, Dennis Doucet, Philippe Rigault, Baohong Zhang, Richard Shen, Celeste McBride, Hai-Ri Li, Xiang-Dong Fu, Arnold Oliphant, David L. Barker, Mark S. Chee (2004), "A versatile assay for high-throughput gene expression profiling on universal array matrices", Genome Research, 14:878-885.
    [abstract]

  66. A Fernandez-Teijeiro, RA Betensky, LM Sturla, JY Kim, P Tamayo, SL Pomeroy (2004), "Combining gene expression profiles and clinical parameters for risk stratification in medulloblastomas", Journal of Clinical Oncology, 22(6):994-998.

  67. affymetrix
    Giacomo Finocchiaro, Paola Parise, Simone P. Minardi, Myriam Alcalay, and Heiko Müller (2004), "GenePicker: replicate analysis of Affymetrix gene expression microarrays", Bioinformatics, 20:3670-3672.

  68. LM Fu, CS Fu-Liu (2004), "Multi-class cancer subtype classification based on gene expression signatures with reliability analysis", FEBS Letters, 561(1-3):186-190.

  69. M Futschik, T Crompton (2004), "Model selection and efficiency testing for normalization of cDNA microarray data", Genome Biology, 5(8):r60.
    [abstract]

  70. G Fleury, A Hero, S Zareparsi, A Swaroop (2004), "Gene discovery using Pareto depth sampling distributions", Journal of Franklin Institute, 341(1-2):55-75.
    [abstract]

  71. affymetrix
    Laurent Gautier, Leslie Cope, Benjamin M. Bolstad, Rafael A Irizarry (2004), "affy--analysis of Affymetrix GeneChip data at the probe level", Bioinformatics, 20(3):307-315.
    [ abstract]

  72. Donald Geman, Christian d'Avignon, Daniel Q. Naiman, Raimond L Winslow (2004), "Classifying gene expression profiles from pairwise mRNA comparisons", Statistical Applications in Genetics and Molecular Biology, 3(1):19.
    [abstract]

  73. database
    RC Gentleman, VJ Carey, DJ Bates, B Bolstad, M Dettling, S Dudoit, B Ellis, L Gautier, Y Ge, J Gentry, K Hornik, T Hothorn, W Huber, S Iacus, R Irizarry, F Leisch, C Li, M Maechler, AJ Rossini, G Sawitzki, C Smith, GK Smyth, L Tierney, YH Yang, J Zhang (2004), "Bioconductor: open software development for computational biology and bioinformatics", Genome Biology. 5:R80.
    [abstract]

  74. Mark Girolami, Rainer Breitling (2004), "Biologically valid linear factor models of gene expression", Bioinformatics, 20:3021-3033.
    [abstract]

  75. Debashis Ghosh (2004), "Mixture models for assessing differential expression in complex tissues using microarray data", Bioinformatics, 20:1663-1669.
    [abstract]

  76. GFV Glonek, PJ Solomon (2004), "Factorial and time course designs for cDNA microarray experiments", Biostatistics, 5:89-111.

  77. G Golfier, M Tran Dang, L Dauphinot, E Graison, J Rossier, MC Potier (2004), "VARAN: a web server for Variability Analysis of DNA microarray experiments", Bioinformatics, 20:1641-1643.
    [abstract]

  78. Jeffrey D Grant, Luke A Somers, Yue Zhang, Frank J Manion, Ghislain Bidaut, Michael F Ochs (2004), "FGDP: functional genomics data pipeline for automated, multiple microarray data analyses", Bioinformatics, 20(2): 282-283.
    [ abstract]

  79. DN Grigoryev, SF Ma, RA Irizarry, SQ Ye, J Quackenbush, JG Garcia (2004), "Orthologous gene-expression profiling in multi-species models: search for candidate genes", Genome Biology, 5(5):R34.

  80. Samir Hanash (2004), "Integrated global profiling of cancer", Nature Reviews Cancer, 4:638-644.

  81. Daniel Handley, Nicoleta Serban, David G. Peters, Clark Glymour (2004), "Concerns about unreliable data from spotted cDNA microarrays due to cross-hybridization and sequence errors" (letters to the editors), Statistical Applications in Genetics and Molecular Biology, 3(1):25.
    [ abstract]

  82. Johanna Hardin, Michael Waddell, C David Page, Fenghuang Zhan, Bart Barlogie, John Shaughnessy, John J Crowley (2004), "Evaluation of multiple models to distinguish closely related forms of disease using DNA microarray data: an application to multiple myeloma", Statistical Applications in Genetics and Molecular Biology, 3(1):10.
    [abstract]

  83. T Hastie, R Tibshirani (2004), "Efficient quadratic regularization for expression arrays", Biostatistics, 5(3):329-340.

  84. Sampsa Hautaniemi, Markus Ringnér, Päivikki Kauraniemi, Reija Autio, Henrik Edgren, Olli Yli-Harja, Jaakko Astola, Anne Kallioniemi, Olli-Pekka Kallioniemi (2004), "A strategy for identifying putative causes of gene expression variation in human cancers", Journal of Franklin Institute, 341(1-2):77-88 .

  85. Peter M. Haverty, Li-Li Hsiao, Steven R. Gullans, Ulla Hansen, Zhiping Weng (2004), "Limited agreement among three global gene expression methods highlights the requirement for non-global validation", Bioinformatics, 20:3431-3441.

  86. Wenqing He (2004), "A spline function approach for detecting differentially expressed genes in microarray data analysis", Bioinformatics, 20:2954-2963. br> [abstract]

  87. Paul Helman, Robert Veroff, Susan R. Atlas, Cheryl Willman (2004), "A Bayesian network classification methodology for gene expression data", Journal of Computational Biology, 11(4):581-615.

  88. Alfred O Hero, Gilles Fleury (2004), "Pareto-optimal methods for gene analysis", Journal of VLSI Signal Processing, ?:?-?.

  89. Alfred O Hero, Gilles Fleury, Alan J Mears, Anand Swaroop (2004), "Multicriteria gene screening for analysis of differential expression with DNA microarrays", EURASIP Journal on Applied Signal Processing, 2004(1):43-52.
    [abstract]

  90. J Herrero, JM Vaquerizas, F Al-Shahrour, L Conde, A Mateos, JS Diaz-Uriarte, J Dopazo (2004), "New challenges in gene expression data analysis and the extended GEPAS", Nucleic Acids Research, 32:W485-491.

  91. Eric P. Hoffman, Tarif Awad, John Palma, Teresa Webster, Earl Hubbell, Janet A. Warrington, Avrum Spira, George Wright, Jonathan Buckley, Tim Triche, Ron Davis, Robert Tibshirani, Wenzhong Xiao Wendell Jones, Ron Tompkins, Mike West (The Tumor Analysis Best Practices Working Group) (2004), "Expression profiling - best practices for data generation and interpretation in clinical trials", Nature Reviews Genetics, 5:229-237.
    [abstract]

  92. Henrik Hornshoj, Henrik Stengaard, Frank Panitz, Christian Bendixen (2004), "SEPON, a Selection and Evaluation Pipeline for OligoNucleotides based on ESTs with a non-target Tm algorithm for reducing cross-hybridization in microarray gene expression experiments", Bioinformatics, 20(3):428-429.
    [ abstract]

  93. Jianping Hua, Zhongmin Liu, Zixiang Xiong, Qiang Wu, Kenneth R Castleman (2004), "Microarray BASICA: background adjustment, segmentation, image compression and analysis of microarray images", EURASIP Journal on Applied Signal Processing, 2004(1):92-107.
    [abstract]

  94. Xiaohong Huang, Wei Pan, Soon Park, Xinqiang Han, Leslie W. Miller, Jennifer Hall (2004), "Modeling the relationship between LVAD support time and gene expression changes in the human heart by penalized partial least squares", Bioinformatics, 20:888-894.
    [abstract]

  95. Kyu-Baek Hwang , Sek Won Kong, Steve A Greenberg, Peter J Park (2004), "Combining gene expression data from different generations of oligonucleotide arrays", BMC Bioinformatics, 5:159.
    [abstract]

  96. Jan H Ihmels, Sven Bergmann (2004), "Challenges and prospects in the analysis of large-scale gene expression data", Briefings in Bioinformatics, 5(4):313-327.

  97. I Inza, P Larrañaga, R Blanco, AJ Cerrolaza (2004), "Filter versus wrapper gene selection approaches in DNA microarray domains", Artificial Intelligence in Medicine, 31(2):91-103.

  98. Anna-Kaarina Jarvinen, Sampsa Hautaniemi, Henrik Edgren, Petri Auvinen, Janna Saarela, Olli-P. Kallioniemi, Outi Monni (2004), "Are data from different gene expression microarray platforms comparable?", Genomics, 83(6):1164-1168.
    [abstract]

  99. Liping Ji, Kian-Lee Tan (2004), "Mining gene expression data for positive and negative co-regulated gene clusters", Bioinformatics, 20(16):2711-2718.
    [abstract]

  100. Xinglai Ji, Yuan Yuan, Jesse Li-Ling, Yanda Li, and Zhirong Sun (2004), "HMMGEP: clustering gene expression data using hidden Markov models", Bioinformatics, 20:1799-1800.
    [abstract]

  101. Daxing Jiang, Jian Pei, Aidong Zhang (2004), "Towards interactive exploration of gene expression patterns", ACM SIGKDD Explorations, 6(1):?-?.

  102. Daxin Jiang, Chun Tang, Aidong Zhang (2004), "Cluster analysis for gene expression data: a survey", IEEE Transactions on Knowledge and Data Engineering, 16(11):1370-1386.
    [abstract]

  103. H Jiang, Y Deng, HS Chen, L Tao, Q Sha, J Chen, CJ Tsai, S Zhang (2004), "Joint analysis of two microarray gene-expression data sets to select lung adenocarcinoma marker genes", BMC Bioinformatics, 5:81.
    [abstract]

  104. Bertrand R Jordan (2004), "How consistent are expression chip platforms?", BioEssays, 26(11):1236-1242.
    [abstract]

  105. M Kapushesky, P Kemmeren, AC Culhane, S Durinck, J Ihmels, C Korner, M Kull, A Torrente, U Sarkans, J Vilo, A Brazma (2005), "Expression Profiler: next generation--an online platform for analysis of microarray data", Nucleic Acids Research, 32(Web Server issue):W465-W470.

  106. database
    Tatiana V. Karpinets, Brent D. Foy, and John M. Frazier (2004), "Tailored gene array databases: applications in mechanistic toxicology", Bioinformatics, 20(4):507-517.
    [abstract]

  107. P Khatri, P Bhavsar, G Bawa, S Draghici (2004), "Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments", Nucleic Acids Research, 32:W449-W456.

  108. database
    Jihoon Kim, Hee-Joon Chung, Chan Hee Park, Woong-Yang Park, Ju Han Kim (2004), "ChromoViz: multimodal visualization of gene expression data onto chromosomes using scalable vector graphics", Bioinformatics, 20:1191-1192.
    [abstract]

  109. Nicholas Knowlton, Igor M. Dozmorov, and Michael Centola (2004), "Microarray Data Analysis Toolbox (MDAT): for normalization, adjustment and analysis of gene expression data", Bioinformatics, 20:3687-3690.

  110. R Konig, D Baldessari, N Pollet, C Niehrs, R Eils (2004), "Reliability of gene expression ratios for cDNA microarrays in multiconditional experiments with a reference design", Nucleic Acids Research, 32(3):e29.

  111. T Konishi (2004), "Three-parameter lognormal distribution ubiquitously found in cDNA microarray data and its application to parametric data treatment", BMC Bioinformatics, 5:5.
    [abstract]

  112. D Kostka, R Spang (2005), "Finding disease specific alterations in the co-expression of genes", Bioinformatics, 20(Suppl 1):I194-I199.

  113. Jeanne Kowalski, Charles Drake, Ronald H. Schwartz, and Jonathan Powell (2004), "Non-parametric, hypothesis-based analysis of microarrays for comparison of several phenotypes", Bioinformatics, 20(3):364-373.
    [ abstract]

  114. David P Kreil, Natasha A Karp, Kathryn S Lilley (2004), "DNA microarray normalization methods can remove bias from differential protein expression analysis of 2D difference gel electrophoresis results", Bioinformatics, 20:2026-2034. [abstract]

  115. Balaji Krishnapuram , Lawrence Carin , Alexander J Hartemink (2004), "Joint classifier and feature optimization for comprehensive cancer diagnosis using gene expression data", Journal of Computational Biology, 11(2-3):227-242.

  116. WP Kuo, EY Kim, J Trimarchi, TK Jenssen, SA Vinterbo, L Ohno-Machado (2005), "A primer on gene expression and microarrays for machine learning researchers", J Biomed Inform., 37(4):293-303.

  117. Zoltan Kutalik, Jacqueline Inwald, Steve V. Gordon, R. Glyn Hewinson, Philip Butcher, Jason Hinds, Kwang-Hyun Cho, Olaf Wolkenhauer (2004), "Advanced significance analysis of microarray data based on weighted resampling: a comparative study and application to gene deletions in Mycobacterium bovis", Bioinformatics, 20(3):357-363.
    [ abstract]

  118. Yinglei Lai, Baolin Wu, Liang Chen, Hongyu Zhao (2004), "A statistical method for identifying differential gene-gene co-expression patterns", Bioinformatics, 20:3146-3155.
    [abstract]

  119. Neil D Lawrence, Marta Milo, Mahesan Niranjan, Penny Rashbass, and Stephan Soullier (2004), "Reducing the variability in cDNA microarray image processing by Bayesian inference", Bioinformatics, 20(4): 518-526.
    [abstract]

  120. Homin K. Lee, Amy K Hsu, Jon Sajdak, Jie Qin, Paul Pavlidis (2004), "Coexpression analysis of human genes across many microarray data sets", Genome Research, 14:1085-1094.

  121. Yoonkyung Lee , Yi Lin , Grace Wahba (2004), "Multicategory support vector machines: theory and application to the classification of microarray data and satellite radiance data", Journal of the American Statistical Association, 99:67-81.

  122. Jorge Lepre, J. Jeremy Rice, Yuhai Tu, Gustavo Stolovitzky (2004), "Genes@Work: an efficient algorithm for pattern discovery and multivariate feature selection in gene expression data", Bioinformatics, 20:1033-1044.
    [abstract]

  123. Hongzhe Li and Jiang Gui (2004), "Partial Cox regression analysis for high-dimensional microarray gene expression data", Bioinformatics, 20:i208-i215.

  124. Tao Li, Chengliang Zhang, and Mitsunori Ogihara (2004), "A comparative study of feature selection and multiclass classification methods for tissue classification based on gene expression", Bioinformatics, 20(15):2429-2437.
    [abstract]

  125. W Li, F Sun, I Grosse (2004), "Extreme-value distribution based gene selection criteria for discriminant microarray data analysis using logistic regression", Journal of Computational Biology, 11(2-3):215-226.

  126. Zheng Li, Christina Chan (2004), "Extracting novel information from gene expression data", Trends in Biotechnology, 22(8):381-383.
    [PDF]

  127. Yulan Liang, Arpad G Kelemen (2004), "Hierarchical Bayesian neural network for gene expression temporal patterns", Statistical Applications in Genetics and Molecular Biology, 3(1):20.
    [abstract]

  128. J.G. Liao, Yong Lin, Zachariah E. Selvanayagam, Weichung Joe Shih (2004), "A mixture model for estimating the local false discovery rate in DNA microarray analysis", Bioinformatics, 20(16):2694-2701.
    [abstract]

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  130. B Liu, Q Cui, T Jiang, S Ma (2005), "A combinational feature selection and ensemble neural network method for classification of gene expression data", BMC Bioinformatics, 5(1):136.
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  131. H Liu, J Li, L Wong (2004), "Selection of patient samples and genes for outcome prediction", Proc IEEE Comput Syst Bioinform Conf., pp.382-392.

  132. Y Liu, M Ringnér (2004), "Multiclass discovery in array data", BMC Bioinformatics, 5:70.
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  133. Feng Luo, Latifur Khan, Farokh Bastani, I-Ling Yen, Jizhong Zhou (2004), "A dynamically growing self-organizing tree (DGSOT) for hierarchical clustering gene expression profiles", Bioinformatics, 20(16):2605-2617.
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  134. SC Madeira, AL Oliveira (2004), "Biclustering algorithms for biological data analysis: a survey", IEEE/ACM Transactions on Computational Biology and Bioinformatics, 1(1):24-45

  135. MZ Man, G Dyson, K Johnson, B Liao (2004), "Evaluating methods for classifying expression data", Journal of Biopharmaceutical Statistics, 14(4):1065-1084.
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  136. database
    E. Manduchi, G. R. Grant, H. He, J. Liu, M. D. Mailman, A. D. Pizarro, P. L. Whetzel, and C. J. Stoeckert, Jr (2004), "RAD and the RAD Study-Annotator: an approach to collection, organization and exchange of all relevant information for high-throughput gene expression studies", Bioinformatics, 20(4):452-459.
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  137. Robert Mansourian, David M. Mutch, Nicolas Antille, Jerome Aubert, Paul Fogel, Jean-Marc Le Goff, Julie Moulin, Anton Petrov, Andreas Rytz, Johannes J. Voegel, and Matthew-Alan Roberts (2004), "The Global Error Assessment (GEA) model for the selection of differentially expressed genes in microarray data", Bioinformatics, 20(16):2726-2737.
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  140. database
    Yohei Minakuchi, Masahiro Ito, Yuji Kohara (2004), "SPI: a tool for incorporating gene expression data into a four-dimensional database of Caenorhabditis elegans embryogenesis", Bioinformatics, 20:1097-1109.
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  142. A Naderi, AA Ahmed, NL Barbosa-Morais, S Aparicio, JD Brenton, C Caldas (2004), "Expression microarray reproducibility is improved by optimising purification steps in RNA amplification and labelling", BMC Genomics, 5(1):9.

  143. Markus Neuhäuser and Roswitha Senske (2004), "The Baumgartner-Weiß-Schindler test for the detection of differentially expressed genes in replicated microarray experiments", Bioinformatics, 20:3553-3564.

  144. Michael A. Newton, Amine Noueiry, Deepayan Sarkar, Paul Ahlquist (2004), "Detecting differential gene expression with a semiparametric hierarchical mixture method", Biostatistics, 5:155-176.

  145. Jens Nilsson, Thoas Fioretos, Mattias Höglund, Magnus Fontes (2004), "Approximate geodesic distances reveal biologically relevant structures in microarray data", Bioinformatics, 20:874-880.
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  147. Minhui Paik, Yuhong Yang (2004), "Combining nearest neighbor classifiers versus cross-validation selection", Statistical Applications in Genetics and Molecular Biology, 3(1):12.
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  148. R Pandey, RK Guru, DW Mount (2004), "Pathway Miner: extracting gene association networks from molecular pathways for predicting the biological significance of gene expression microarray data", Bioinformatics, 20:2156-2158.

  149. G Parmigiani, ES Garrett-Mayer, R Anbazhagan, E Gabrielson (2004), "A cross-study comparison of gene expression studies for the molecular classification of lung cancer", Clin Cancer Res. 10(9):2922-2927.

  150. C. Pasquier, F. Girardot, K. Jevardat de Fombelle, R. Christen (2004), "THEA: ontology-driven analysis of microarray data", Bioinformatics, 20(16):2636-2643.
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  157. affymetrix
    Nancie Reymond, Hubert Charles, Laurent Duret, Federica Calevro, Guillaume Beslon, Jean-Michel Fayard (2004), "ROSO: optimizing oligonucleotide probes for microarrays", Bioinformatics, 20(2): 271-273.
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  162. application
    JE Robison, L Perreard, PS Bernard (2004), "State of the science: molecular classifications of breast cancer for clinical diagnostics", Clinical Biochemistry, 37(7):572-578.

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  164. Alok J. Saldanha (2004), "Java Treeview-extensible visualization of microarray data", Bioinformatics, 20:3246-3248.
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  166. affymetrix
    Jinwook Seo, Marina Bakay, Yi-Wen Chen, Sara Hilmer, Ben Shneiderman, Eric P Hoffman (2004), "Interactively optimizing signal-to-noise ratios in expression profiling: project-specific algorithm selection and detection p-value weighting in Affymetrix microarrays", Bioinformatics, 20(16):2534-2544.
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  169. Marcel Smid, Lambert C. J. Dorssers (2004), "GO-Mapper: functional analysis of gene expression data using the expression level as a score to evaluate Gene Ontology terms", Bioinformatics, 20(16):2618-2625.
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  172. Radka Stoyanova, Troy D. Querec, Truman R. Brown, and Christos Patriotis (2004), "Normalization of single-channel DNA array data by principal component analysis", Bioinformatics, 20:1772-1784.
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  173. A Szabo, CM Perou, M Karaca, L Perreard, JF Quackenbush, PS Bernard (2004), "Statistical modeling for selecting housekeeper genes", Genome Biology, 5(8):R59.
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  175. affymetrix
    Ziad Taib (2004), "Statistical analysis of oligonucleotide microarray data" ("Analyse statistique de données de puces d'ADN à base d'oligonucléotides) Comptes Rendus Biologies, 327(3):175-180
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  176. Chun Tang, Aidong Zhang, Murali Ramanathan (2004), "ESPD: a pattern detection model underlying gene expression profiles", Bioinformatics, 20:829-838.
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  177. Yongxi Tan, Leming Shi, Weida Tong, GT Gene Hwang, Charles Wang (2004), "Multi-class tumor classification by discriminant partial least squares using microarray gene expression data and assessment of classificaition models", Computational Biology and Chemistry, 28:235-244.

  178. CA Tsai, JJ Chen (2005), "Significance analysis of ROC indices for comparing diagnostic markers: applications to gene microarray data", J Biopharm Stat., 14(4):985-1003.

  179. CA Tsai, CH Chen, TC Lee, IC Ho, UC Yang, JJ Chen (2005), "Gene selection for sample classifications in microarray experiments", DNA Cell Biol., 23(10):607-614.

  180. CA Tsai, HM Hsueh, JJ Chen (2005), "A generalized additive model for microarray gene expression data analysis", J Biopharm Stat., 14(3):553-573.

  181. Juan M Vaquerizas, Joaquín Dopazo, and Ramón Díaz-Uriarte (2004), "DNMAD: web-based diagnosis and normalization for microarray data", Bioinformatics, 20:3656-3658.

  182. Joseph S Verducci, Vincent F Melfi, Shili Lin, Zailong Wang, Sashwati Roy, Chandan K Sen (2004), "Microarray analysis of gene expression: considerations in data mining and statistical treatment", Physiological Genomics, 25:355-363.
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  183. J Wang, KR Coombes, WE Highsmith, MJ Keating, LV Abruzzo (2004), "Differences in gene expression between B-cell chronic lymphocytic leukemia and normal B cells: a meta-analysis of three microarray studies", Bioinformatics, 20:3166-3178.
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  184. Song Wang, Stewart Ethier (2004), "A generalized likelihood ratio test to identify differentially expressed genes from microarray data", Bioinformatics, 20:100-104.
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  185. Sue-Jane Wang, James J. Chen (2004), "Sample size for identifying differentially expressed genes in microarray experiments", Journal of Computational Biology, 11(4):714-726.

  186. James M. Wettenhall and Gordon K. Smyth (2004), "limmaGUI: A graphical user interface for linear modeling of microarray data", Bioinformatics, 20:3705-3706.

  187. Sofia Wichert, Konstantinos Fokianos, Korbinian Strimmer (2004), "Identifying periodically expressed transcripts in microarray time series data", Bioinformatics, 20:5-20.
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  188. affymetrix
    Y Woo, J Affourtit, S Daigle, A Viale, K Johnson, J Naggert, G Churchill (2004), "A comparison of cDNA, oligonucleotide, and Affymetrix GeneChip gene expression microarray platforms", J Biomol Tech. 15(4):276-284.

  189. Wren JD, Yao M, Langer M, Conway T (2004), "Simulated annealing of microarray data reduces noise and enables cross-experimental comparisons", DNA Cell Biol., 23(10):695-700.

  190. Xiongwu Wu, Yidong Chen, Bernard R Brooks, Yan A Su (2004), "The local maximum clustering method and its application in microarray gene expression data analysis", EURASIP Journal on Applied Signal Processing, 2004(1):53-63.
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  191. affymetrix
    Z Wu, RA Irizarry (2004), "Stochastic models inspired by hybridization theory for short oligonucleotide arrays", Proceedings of the Eighth International Conference on Research in Computational Molecular Biology , pp.?-?.

  192. D Yang, SO Zakharkin, GP Page, JP Brand, JW Edwards, AA Bartolucci, DB Allison (2004), "Applications of Bayesian statistical methods in microarray data analysis", American Journal of Pharmacogenomics, 4(1):53-62.

  193. B Yao, SN Rakhade, Q Li, S Ahmed, R Krauss, S Draghici, JA Loeb (2004), "Accuracy of cDNA microarray methods to detect small gene expression changes induced by neuregulin on breast epithelial cells", BMC Bioinformatics, 5(1):99.
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  196. Barry R Zeeberg, Joseph Riss, David W Kane, Kimberly J Bussey, Edward Uchio, Marston Linehan, J Carl Barrett, John N Weinstein (2004), "Mistaken identifiers: gene name errors can be introduced inadvertently when using Excel in bioinformatics", BMC Bioinformatics, 5:80.
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  197. Li Zhang, Aidong Zhang, Murali Ramanathan (2004), "VizStruct: exploratory visualization for gene expression profiling", Bioinformatics, 20(1):85-92.

  198. Shu-Dong Zhang, Timothy W. Gant (2004), "A statistical framework for the design of microarray experiments and effective detection of differential gene expression", Bioinformatics, 20(16):2821-2828.
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  199. networks
    Xiaobo Zhou, Xiaodong Wang, Edward R. Dougherty (2004), "Gene prediction using multinomial probit regression with Bayesian gene selection", EURASIP Journal on Applied Signal Processing, 2004(1):115-124.
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  200. Xiaobo Zhou, Xiaodong Wang, Edward R. Dougherty (2004), "A Bayesian approach to nonlinear probit gene selection and classification", Journal of Franklin Institute, 341(1-2):137-156.

  201. J Zhu, T Hastie (2004), "Classification of gene microarrays by penalized logistic regression", Biostatistics, 5(3):427-443.
2004